Objectives: This paper examines the workflow of sleep physicians during a patient consultation and how an innovative clinical decision support system (CDSS) provides efficiency and effectiveness gains. Methods: The CDSS tools consisted of two input applications for patient data, with a knowledge based decision support system developed participatively with physicians and an international panel. An argument tree approach was used to produce diagnostic explanations and an evidence-based report for the physician using medically correct and shared terminology. A usability evaluation using a qualitative approach was carried out to ensure that the CDSS met the physicians’ information needs, as well as the wider needs of a Sleep Investigation Unit. Results: The physicians found the CDSS both useful and usable with clear applications in triage and diagnostic decision-making, and in patient education. Conclusion: The CDSS both reduces the time and number of visits needed for consultations, and helps focus consultation on better individual patient care through informed explanation of diagnostic and treatment decisions.